[R-pkg-devel] "try" malfunctions on Ubuntu Linux 16.04 LTS, R-release, GCC
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
Mon Feb 3 03:47:52 CET 2020
Maybe an Rhub glitch. I just ran R CMD check with a recent r-devel
(2019-12-03 r77509) on Ubuntu 16.04 with no problems.
On 2020-02-02 9:15 p.m., Spencer Graves wrote:
> Hello, All:
>
>
> devtools::check_rhub failed to trap an error wrapped in "try",
> per the email below. This came from running
> devtools::check_rhub(Ecfun_dir), where Ecfun_dir = the path to a copy of
> "https://github.com/sbgraves237/Ecfun".
>
>
> This is the development version of Ecfun, which I want to submit
> to CRAN as soon as I can do so without offending the sensibilities of
> the overworked CRAN maintainers.
>
>
> Suggestions?
> Thanks,
> Spencer Graves
>
>
> -------- Forwarded Message --------
> Subject: Ecfun 0.2-2: ERROR
> Date: Sun, 02 Feb 2020 23:27:10 +0000
> From: R-hub builder <support using rhub.io>
> To: spencer.graves using effectivedefense.org
>
>
>
> Ecfun 0.2-2: ERROR
>
>
> Ecfun 0.2-2: ERROR
> *Build ID:* |Ecfun_0.2-2.tar.gz-a5518fc2c19c4cd191a5d67b55c45603|
> *Platform:* Ubuntu Linux 16.04 LTS, R-release, GCC
> *Submitted:* 1 hour 55 minutes 18.7 seconds ago
> *Build time:* 1 hour 49 minutes 23.6 seconds
>
>
> ERRORS:
>
> * checking examples ... ERROR
> Running examples in ‘Ecfun-Ex.R’ failed
> The error most likely occurred in:
>
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: interpPairs
>> ### Title: interpolate between pairs of vectors in a list
>> ### Aliases: interpPairs interpPairs.call interpPairs.function
>> ### interpPairs.list
>> ### Keywords: manip
>>
>> ### ** Examples
>>
>> ###
>> ###
>> ### 1. interpPairs.function
>> ###
>> ###
>>
>> ##
>> ## 1.1. simple
>> ##
>> plot0 <- quote(plot(0))
>> plot0. <- interpPairs(plot0)
>> # check
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(plot0, plot0.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 1.2. no op
>> ##
>> noop <- interpPairs(plot0, iFrame=-1)
>> # check
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(noop, enquote(NULL))
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 1.3. a more typical example
>> ## example function for interpPairs
>> tstPlot <- function(){
> + plot(1:2, 1:2, type='n')
> + lines(firstFrame=1:3,
> + lastFrame=4,
> + x.1=seq(1, 2, .5),
> + y.1=x,
> + z.0=0, z.1=1,
> + txt.1=c('CRAN is', 'good', '...'),
> + col='red')
> + }
>> tstbo <- body(tstPlot)
>> iPlot <- interpPairs(tstbo[[2]])
>> # check
>> iP <- quote(plot(1:2, 1:2, type='n'))
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(iPlot, iP)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> iLines <- interpPairs(tstbo[[3]], nFrames=5, iFrame=2)
>> # check:
>> # .proportion = (iFrame-firstFrame)/(lastFrame-firstFrame)
>> # = c(1/3, 0, -1/3)
>> # if x.0 = 0 and y.0 = 0 by default:
>> iL <- quote(linex(x=c(1/3, 0), y=c(1/9, 0), z=c(1/3, 0),
> + tst=c('CR', '')))
>> ##
>> ##**** This example seems to give the wrong answer
>> ##**** 2014-06-03: Ignore for the moment
>> ##
>> #all.equal(iLines, iL)
>>
>> ##
>> ## 1.4. Don't throw a cryptic error with NULL
>> ##
>> ip0 <- interpPairs(quote(text(labels.1=NULL)))
>>
>>
>> ###
>> ###
>> ### 2. interpPairs.list
>> ###
>> ###
>>
>> ##
>> ## 2.1. (x.0, y.0, x.1, y.1) -> (x,y)
>> ##
>> tstList <- list(x.0=1:5, y.0=5:9, y.1=9:5, x.1=9,
> + ignore=letters, col=1:5)
>> xy <- interpPairs(tstList, 0.1)
>> # check
>> xy. <- list(ignore=letters, col=1:5,
> + x=1:5 + 0.1*(9-1:5),
> + y=5:9 + 0.1*(9:5-5:9) )
>> # New columns, 'x' and 'y', come after
>> # columns 'col' and 'ignore' already in tstList
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(xy, xy.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 2.2. Select the middle 2:
>> ## x=(1-(0,1))*3:4+0:1*0=(3,0)
>> ##
>> xy0 <- interpPairs(tstList[-4], c(-Inf, -1, 0, 1, 2) )
>> # check
>> xy0. <- list(ignore=letters, col=3:4, x=c(3,0), y=7:6)
>>
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(xy0, xy0.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>> ##
>> ## 2.3. Null interpolation because of absence of y.1 and x.0
>> ##
>> xy02 <- interpPairs(tstList[c(2, 4)], 0.1)
>> # check
>> #### NOT the current default answer; revisit later.
>> xy02. <- list(y=5:9, x=9)
>>
>> # NOTE: length(x) = 1 = length(x.1) in testList
>> #all.equal(xy02, xy02.)
>>
>> ##
>> ## 2.4. Select an empty list (make sure this works)
>> ##
>> x0 <- interpPairs(list(), 0:1)
> Warning message:
> In checkNames(object, avoid = pairs[c(1, 4, 2, 5)]) :
> object: names = NULL; returning make.names(character(length(x))), TRUE)
>> # check
>> x0. <- list()
>> names(x0.) <- character(0)
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(x0, x0.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 2.5. subset one vector only
>> ##
>> xyz <- interpPairs(list(x=1:4), c(-1, 0, 1, 2))
>> # check
>> xyz. <- list(x=2:3)
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(xyz, xyz.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 2.6. with elements of class call
>> ##
>> xc <- interpPairs(list(x=1:3, y=quote(x+sin(pi*x/6))), 0:1)
>> # check
>> xc. <- list(x=1:3, y=quote(x+sin(pi*x/6)))
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(xc, xc.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 2.7. text
>> ##
>> # 2 arguments
>> j.5 <- interpPairs(list(x.0='', x.1=c('a', 'bc', 'def')), 0.5)
>> # check
>> j.5. <- list(x=c('a', 'bc', ''))
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(j.5, j.5.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 2.8. text, 1 argument as a list
>> ##
>> j.50 <- interpPairs(list(x.1=c('a', 'bc', 'def')), 0.5)
>> # check
>> ## Don't show:
>> stopifnot(
> + ## End(Don't show)
> + all.equal(j.50, j.5.)
> + ## Don't show:
> + )
>> ## End(Don't show)
>>
>> ##
>> ## 2.9. A more complicated example with elements to eval
>> ##
>> logo.jpg <- paste(R.home(), "doc", "html", "logo.jpg",
> + sep = .Platform$file.sep)
>> if(require(jpeg)){
> + Rlogo <- try(readJPEG(logo.jpg))
> + if(!inherits(Rlogo, 'try-error')){
> + # argument list for a call to rasterImage or rasterImageAdj
> + RlogoLoc <- list(image=Rlogo,
> + xleft.0 = c(NZ=176.5,CH=172,US=171,
> + CN=177,RU= 9.5,UK= 8),
> + xleft.1 = c(NZ=176.5,CH= 9,US=-73.5,
> + CN=125,RU= 37, UK= 2),
> + ybottom.0=c(NZ=-37, CH=-34,US=-34,
> + CN=-33,RU= 48, UK=47),
> + ybottom.1=c(NZ=-37, CH= 47,US= 46,
> + CN= 32,RU=55.6,UK=55),
> + xright=quote(xleft+xinch(0.6)),
> + ytop = quote(ybottom+yinch(0.6)),
> + angle.0 =0,
> + angle.1 =c(NZ=0,CH=3*360,US=5*360,
> + CN=2*360,RU=360,UK=360)
> + )
> +
> + RlogoInterp <- interpPairs(RlogoLoc,
> + .proportion=rep(c(0, -1), c(2, 4)) )
> + # check
> + ## Don't show:
> + stopifnot(
> + ## End(Don't show)
> + all.equal(names(RlogoInterp),
> + c('image', 'xright', 'ytop', 'xleft', 'ybottom', 'angle'))
> + ## Don't show:
> + )
> + ## End(Don't show)
> + }
> + # NOTE: 'xleft', and 'ybottom' were created in interpPairs,
> + # and therefore come after 'xright' and 'ytop', which were
> + # already there.
> +
> + ##
> + ## 2.10. using envir
> + ##
> + RlogoDiag <- list(x0=quote(Rlogo.$xleft),
> + y0=quote(Rlogo.$ybottom),
> + x1=quote(Rlogo.$xright),
> + y1=quote(Rlogo.$ytop) )
> +
> + RlogoD <- interpPairs(RlogoDiag, .p=1,
> + envir=list(Rlogo.=RlogoInterp) )
> + ## Don't show:
> + stopifnot(
> + ## End(Don't show)
> + all.equal(RlogoD, RlogoDiag)
> + ## Don't show:
> + )
> + ## End(Don't show)
> + }
> Loading required package: jpeg
> Error in readJPEG(logo.jpg) : unable to open /usr/lib/R/doc/html/logo.jpg
> Error in interpPairs.list(RlogoDiag, .p = 1, envir = list(Rlogo. = RlogoInterp)) :
> object 'RlogoInterp' not found
> Calls: interpPairs -> interpPairs.list
> Execution halted
>
>
> NOTES:
>
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ‘Spencer Graves<spencer.graves using effectivedefense.org>’
>
> Found the following (possibly) invalid URLs:
> URL:https://www.measuringworth.com/
> From: inst/doc/UpdatingUSGDPpresidents.html
> Status: Error
> Message: libcurl error code 60:
> SSL certificate problem: unable to get local issuer certificate
> (Status without verification: OK)
>
> * checking Rd cross-references ... NOTE
> Packages unavailable to check Rd xrefs: ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘TRAMPR’
>
> See the full build log: HTML
> <https://builder.r-hub.io/status/Ecfun_0.2-2.tar.gz-a5518fc2c19c4cd191a5d67b55c45603>,
> text
> <https://builder.r-hub.io/status/original/Ecfun_0.2-2.tar.gz-a5518fc2c19c4cd191a5d67b55c45603>,
> artifacts
> <https://artifacts.r-hub.io/Ecfun_0.2-2.tar.gz-a5518fc2c19c4cd191a5d67b55c45603>.
>
> Have questions, suggestions or want to report a bug? Please file an
> issue ticket at GitHub <https://github.com/r-hub/rhub/issues>. Thank You
> for using the R-hub builder.
>
> (c) 2016 The R Consortium
>
>
>
>
> [[alternative HTML version deleted]]
>
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